However, in 2372, the crew of USS Voyager discovered a new form of dilithium that could remain stable at a much higher warp frequency, and modified the Class 2 shuttle to achieve high-warp engine performance, reaching significantly past warp 9. (VOY: "Threshold")

According to Tom Paris, the decision to construct the Delta Flyer was based on the fact that "class-2 shuttles just don't cut it in the Delta Quadrant." He added that "we've needed something bigger and better since we got here." (VOY: "Drone", "Extreme Risk")

This type of shuttlecraft was consistently referred to as a "class-2 shuttle" on-screen. In "Resolutions", a reference was made to a "type-9 shuttle" that was never shown in the episode. According to Star Trek Encyclopedia (3rd ed p.443) the "type-9 shuttlecraft" is the class 2 shuttle. However, Rick Sternbach designed this shuttle as the "type-12 shuttlecraft". Star Trek: The Next Generation Technical Manual (p.162) used the designation type-9A to indicate a large long-range cargo shuttle.

The design of the shuttle originated from the desire of the art department to introduce a "cool and sleek shuttle", but the opportunity only presented itself when "Threshold" entered pre-production. Sternbach was charged with designing the new shuttle early summer 1995. "We knew that "cool and sleek" was going to mean long, low and streamlined, but we also had to insure that our actors could stand up inside, so the minimum ceiling height was kept at almost six feet. If we were required to make the speedboat as sleek as, say a Lotus or Ferrari automobile, they'd have to crouch inelegantly to enter their seats," Sternbach remembers. Working closely with production designer Richard James and set designer John Chichester in order to match interior with exterior, he was able to come up early with a design that approximated the final look of the shuttle, which was very soon dubbed by the art department staff as the "Speedboat Shuttle," a name also adopted by fans. The design was a break from the established look for Starfleet shuttles, which until then were variations of the classic box shaped design. Further detailing and refining meant that Sternbach was only able to produce blueprints in November 1995 for forwarding to Tony Meininger's Brazil-Fabrication & Design where the physical studio model was built. Since Star Trek: Voyager was in the middle of the process of transition to CGI, it proved to be the last physical shuttle model built for the show and no full scale mock-up was ever built. (Star Trek: The Magazine Volume 2, Issue 5)